The Rappid bootloader does not use a pin to tell the bootloader if bootloader or application should start.

After reset, the Rappid bootloader is always started. The bootloader starts to search for valid boot header (part of application image). See please user manual and release notes for details. There’s RCHW, start address, delay and app key in this section. If valid boot header is found, the bootloader waits for defined delay (value defined in boot header) – if Rappid Bootloader (application running on PC) sends a request for update during this delay then bootloader is started and we can update user application (or read the flash memory or erase the flash memory). If the request is not received then user application is started.

If this bootloader is not sufficient for you, it is necessary to develop own bootloader. Here is an example of such bootloader:

I wrote this for PowerPC devices but the principle is the same. I’m sharing this just to have clue how it works. If you write own bootloader, you can use any condition to start the bootloader (state of GPIO pin after reset, command received via serial interface, key in the flash memory…).